UV Maps and inconsistent shading issues
That indeed sounds strange.
What do you mean with export? As .blend file? To another program?

"Are all the islands supposed to be oriented in relation to one another?" - No except that they shouldn't overlap.

Did you bake your textures previously? (then that might have been the problem, because the lighting is set before you rotated)

Uploading some screenshots or a .blend file might help to solve the problem ;)